[gmx-users] restart issues with Gromacs

Mark Abraham mark.j.abraham at gmail.com
Sun Nov 15 23:12:43 CET 2015


GROMACS assumes the file systems actually write to disk when you use the
system call that means that, and works correctly if so. But if the file
system or its configuration don't actually do that (for "performance" or
erroneous reasons), then all bets are off. mdrun can't even know if it's
being lied to, because, well, it's being lied to...


On Sun, 15 Nov 2015 22:30 Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> Hi all,
> Running Grimaces 5.0.4 with PLUMED 2.2 on a cluster, number of ranks (MPI
> processes) is 24. The simulation successfully ran for the maximum cluster
> wall time (48 hours).
> I attempt to restart the simulations using the following command (with a
> sun microsystem grid engine submission script):
> gerun mdrun_mpi_d -deffnm neu_mut_meta_K -cpi neu_mut_meta_K.cpt -noappend
> -plumed
> However, whilst the queue is telling me that the job is running, the
> *.part0002.log file seems stuck at:
> -----------------------------------
> When dynamic load balancing gets turned on, these settings will change to:
> The maximum number of communication pulses is: X 1 Y 1
> The minimum size for domain decomposition cells is 1.025 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.43 Y 0.56
> The maximum allowed distance for charge groups involved in interactions is:
>                  non-bonded interactions           1.025 nm
>             two-body bonded interactions  (-rdd)   1.025 nm
>           multi-body bonded interactions  (-rdd)   1.025 nm
>   atoms separated by up to 5 constraints  (-rcon)  1.025 nm
> ------------------------------------
> The cluster error file and output file (not gromacs file) contains no
> warnings or errors. The gromacs log file contains no warnings or errors.
> I have seen this behaviour quite a number of times, going back to early
> versions of gromacs 4 around late 2010 (I think). I got into the habit of
> a) copying backing up the .cpt files, and b) always using -noappend option
> to preserve the .trr file. Has there ever been an explanation as to why
> this is happening?
> Many thanks
> Anthony
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list